☰ Navigation Tabs
XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N6H PDB entry 4N6H, PDB entry 4EIY experimental model PDB 4EIY PDB entry 4N6H, PDB entry 4EIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 293 0.1M MES pH 6.0, 10-180mM Lithium citrate, 30-32% (v/v) PEG400, Lipidic cubic phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.23 α = 90 b = 89.29 β = 92.3 c = 96.42 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 294 PIXEL Cornell-SLAC Pixel Array Detector (CSPAD) 2014-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.6 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 33.5 100 0.118 6 560 36838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.879 1.3 209
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4N6H, PDB entry 4EIY 2.7 33.45 34699 1831 99.92 0.20973 0.20827 0.2114 0.23803 0.2372 RANDOM 64.361
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.77 0.2 -0.41 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.909 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_4_deg 11.068 r_long_range_B_refined 5.074 r_long_range_B_other 5.074 r_dihedral_angle_1_deg 4.382 r_scangle_other 3.501 r_mcangle_it 3.152 r_mcangle_other 3.152 r_scbond_it 2.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.909 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_4_deg 11.068 r_long_range_B_refined 5.074 r_long_range_B_other 5.074 r_dihedral_angle_1_deg 4.382 r_scangle_other 3.501 r_mcangle_it 3.152 r_mcangle_other 3.152 r_scbond_it 2.102 r_scbond_other 2.102 r_mcbond_it 1.939 r_mcbond_other 1.939 r_angle_refined_deg 1.002 r_angle_other_deg 0.848 r_chiral_restr 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6163 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 136
Software Software Software Name Purpose PHASER phasing REFMAC refinement CrystFEL data reduction CrystFEL data scaling